Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

In Search of a Molecular View of Peptide-Lipid Interactions in Membranes.

Langmuir : the ACS journal of surfaces and colloids·2023

Same author

The Antibiotic Peptide Daptomycin Functions by Reorganizing the Membrane.

The Journal of membrane biology·2021

Same author

How to Determine Lipid Interactions in Membranes from Experiment Through the Ising Model.

Langmuir : the ACS journal of surfaces and colloids·2018

Same author

Net Interactions That Push Cholesterol Away from Unsaturated Phospholipids Are Driven by Enthalpy.

Biochemistry·2018

Same author

Heat Capacity of DPPC/Cholesterol Mixtures: Comparison of Single Bilayers with Multibilayers and Simulations.

Langmuir : the ACS journal of surfaces and colloids·2018

Same author

Bacterial glycerol oxidation coupled to sulfate reduction at neutral and acidic pH.

The Journal of general and applied microbiology·2017

Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 7, 2026

Assembly of Cell Mimicking Supported and Suspended Lipid Bilayer Models for the Study of Molecular Interactions

Assembly of Cell Mimicking Supported and Suspended Lipid Bilayer Models for the Study of Molecular Interactions

Published on: August 3, 2021

Tools for predicting binding and insertion of CPPs into lipid bilayers.

Paulo F Almeida¹

¹Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC, USA.

Methods in Molecular Biology (Clifton, N.J.)

|November 6, 2010

Summary

This summary is machine-generated.

Predicting cell-penetrating peptide (CPP) binding and membrane insertion saves time in CPP design. This study details methods using Wimley-White hydrophobicity scales and electrostatic estimations for accurate property prediction.

More Related Videos

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Related Experiment Videos

Last Updated: Jun 7, 2026

Assembly of Cell Mimicking Supported and Suspended Lipid Bilayer Models for the Study of Molecular Interactions

Assembly of Cell Mimicking Supported and Suspended Lipid Bilayer Models for the Study of Molecular Interactions

Published on: August 3, 2021

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Area of Science:

Biophysical Chemistry
Computational Biology
Drug Delivery

Background:

Designing effective cell-penetrating peptides (CPPs) requires accurate prediction of their properties.
Existing methods for predicting CPP behavior, such as membrane insertion and binding, can be time-consuming and complex.

Purpose of the Study:

To present computational methods for predicting CPP binding and membrane insertion.
To demonstrate the utility of Wimley-White hydrophobicity scales and electrostatic estimations for CPP property prediction.

Main Methods:

Utilized Wimley-White hydrophobicity scales for calculating peptide properties.
Incorporated electrostatic effect estimations to refine predictions.
Developed a procedure for estimating the probability of peptide insertion into membranes.

Main Results:

The described methods provide accurate approximations for CPP binding and membrane insertion.
Calculations were validated against experimental data for several CPPs.
The approach offers a time-saving asset for designing novel CPPs.

Conclusions:

Computational methods based on hydrophobicity and electrostatics can reliably predict CPP properties.
These predictive tools are valuable for accelerating the design and development of new CPPs.
The study validates the use of Wimley-White scales and electrostatic approximations in CPP research.